Conformational study of cis-1,4-di-tert-butylcyclohexane by dynamic NMR spectroscopy and computational methods. Observation of chair and twist-boat conformations

Molecular Simulation of Cyclohexane in Nanoporous Materials: Adsorption of Conformers and Coadsorption with Water and Carbon Dioxide

Molecular simulation is used to investigate the adsorption of an organic molecule and its different conformers into various nanoporous adsorbents. In more detail, we perform grand canonical Monte Carlo simulations to determine the adsorption isotherms for cyclohexane with its three conformers (chair, boat, and twisted boat) at three different temperatures into a molecular model of active carbons and two metal-organic frameworks (MOFs) (Cu-BTC and Al-Fum). By considering the adsorption of each conformer separately, we show that the adsorption isotherms are weakly dependent on the molecular conformation. When considering the concomitant adsorption of the three conformers under realistic conditions (to verify the population of each conformer in bulk mixtures), we show that the chair conformer is predominantly adsorbed in each material. However, such favorable adsorption mostly reflects the fact that this conformer has the largest population in the bulk mixture under the same thermodynamic conditions. On the contrary, with an increase in the cyclohexane gas pressure, the adsorption of boat and twisted boat conformers increases, while that of the chair conformer decreases as packing (entropy) effects become predominant during confinement. The adsorption of cyclohexane in the active carbon and MOF materials is also considered in the presence of water and CO2 atmospheres. In the case of the Al-fumarate material, the material is found to be strongly organophilic so that water and CO2 adsorption are negligible, and cyclohexane adsorption is not affected by competitive adsorption under any considered thermodynamic condition. On the contrary, for the active carbon and Cu-BTC material, competitive adsorption between cyclohexane and water or CO2 is observed even if cyclohexane adsorption remains preferred. While the different molecules coexist in the adsorbed phase at low pressures, increasing the cyclohexane pressure beyond 103 Pa promotes cyclohexane adsorption concomitantly with water and/or CO2 desorption.

Driving tert-butyl axial: the surprising cyclopropyl effect

The presence of a small spirocyclic ring at an adjacent position alters the conformational preference for equatorial substitution in six-membered rings. DFT calculations and low-temperature 1H NMR experiments demonstrate that alkyl groups larger than methyl possess negative A-values when geminal to a spirocyclopropane, with larger groups such as isopropyl and tert-butyl being exclusively axial at -78 °C. Similar effects are found for heteroatoms, including halogens, and for a range of other electron-withdrawing substituents. Similar effects are observed for other strained rings (epoxide, cyclobutane, oxetane) and the concepts extend to acyclic models as well as heterocycles such as piperidines and piperazines. The origin of the effect is traced to an increase in torsional strain in combination with hyperconjugative effects in the case of electron-poor groups.

Near-90° Switch in the Polar Axis of Dion-Jacobson Perovskites by Halide Substitution

Ferroelectricity in two-dimensional hybrid (2D) organic-inorganic perovskites (HOIPs) can be engineered by tuning the chemical composition of the organic or inorganic components to lower the structural symmetry and order-disorder phase change. Less efforts are made toward understanding how the direction of the polar axis is affected by the chemical structure, which directly impacts the anisotropic charge order and nonlinear optical response. To date, the reported ferroelectric 2D Dion-Jacobson (DJ) [PbI₄]^2- perovskites exhibit exclusively out-of-plane polarization. Here, we discover that the polar axis in ferroelectric 2D Dion-Jacobson (DJ) perovskites can be tuned from the out-of-plane (OOP) to the in-plane (IP) direction by substituting the iodide with bromide in the lead halide layer. The spatial symmetry of the nonlinear optical response in bromide and iodide DJ perovskites was probed by polarized second harmonic generation (SHG). Density functional theory calculations revealed that the switching of the polar axis, synonymous with the change in the orientation of the sum of the dipole moments (DMs) of organic cations, is caused by the conformation change of organic cations induced by halide substitution.

Recent advances in structures and applications of coordination polymers based on cyclohexanepolycarboxylate ligands

Coordination polymers (CPs) are emerging crystalline materials constructed by metal entities and organic ligands through coordination bonds, containing infinite coordination units in one, two, or three dimensions. Here an overview...

Dynamics and Entropy of Cyclohexane Rings Control pH-Responsive Reactivity

Activation entropy (ΔS ^‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring compounds is mainly determined by the ΔS ^‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ^‡ of 16.02 cal·mol^-1·K^-1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.

Cyclic monoterpenes trapped in a polyaromatic capsule: unusual selectivity, isomerization, and volatility suppression

Cyclic monoterpenes (CMTs) are intractable natural products with high volatility and strong odors so that there has been no molecular receptor capable of selectively and tightly trapping CMTs in both solution and the solid state. We herein report that a polyaromatic capsule acts as a functional nanoflask for CMTs with the following five features: (i) the capsule can selectively bind menthone from mixtures with other saturated CMTs in water. In contrast, (ii) treatment of the capsule with mixtures of menthone and π-conjugated CMTs gives rise to ternary host–guest complexes with high pair-selectivity. Notably, (iii) the encapsulated menthone displays unusual isomerization from a typical chair conformer to otherwise unstable conformers upon heating. (iv) The selective binding of volatilized CMTs is demonstrated by the capsule even in the solid state at atmospheric pressure. Furthermore, (v) the volatilities of CMTs are significantly suppressed at elevated temperatures by the capsule upon encapsulation in solution as well as in the solid state.

A polyaromatic capsule demonstrated its unique host functions toward cyclic monoterpenes, i.e., selective binding in water, pair-selective encapsulation, unusual isomerization, selective binding in the solid state, and remarkable volatility suppression.

Raise the anchor! Synthesis, X-ray and NMR characterization of 1,3,5-triazinanes with an axial tert-butyl group

N-t-Bu-N',N''-Disulfonamide-1,3,5-triazinanes were synthesized and characterized by X-ray single crystal structure analysis. In the course of the X-ray structure elucidation, the first solid experimental evidence of the axial position of the tert-butyl group in unconstrained hexahydro-1,3,5-triazacyclohexanes was obtained. Dynamic low-temperature NMR analysis allowed to fully investigate a rare case of crystallization-driven unanchoring of the tert-butyl group in the chair conformation of saturated six-membered cycles. DFT calculations show that the use of explicit solvent molecules is necessary to explain the equatorial position of the t-Bu group in solution. Otherwise, the axial conformer is the thermodynamically stable isomer.

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein–ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0.

Adsorption of Cyclohexane in Pure Silica Zeolites: High-Throughput Computational Screening Validated by Experimental Data

Adsorption of cyclohexane in pure silica zeolites was studied experimentally and by molecular simulations. Based on the adsorption isobars obtained from the quasi-equilibrated temperature adsorption and desorption (QE-TPDA) measurements and reported adsorption isotherms for high-silica zeolites Y, ZSM-5, and ZSM-11 we refined Lennard-Jones parameters for guest-host interactions available in the literature. Adsorption of cyclohexane from equimolar mixture of twisted-boat and chair conformations has been screened in 171 pure silica zeolitic structures using grand canonical Monte Carlo simulations. Almost 20 frameworks showing extraordinary preference for adsorption of the chair conformation over the twisted boat one or vice versa were found. This selectivity was attributed to the geometry of channels and cavities present in the pore structures, as all t-boat selective structures possess channels or cavities of 8.3-9.1 Å. We also differentiated ways of chair-selectivity depending on the size and shape of the channels or cavities and also on the arrangement of the guest molecules in the pores.

Characterization of Nine Isomers in Commercial Samples of Perfluoroethylcyclohexanesulfonate and of Some Minor Components Including PFOS Isomers

Electrochemical fluorination of 4-ethylbenzenesulfonyl halides produces a mixture of compounds that has found extensive use as an erosion inhibitor in aircraft hydraulic fluids. This paper reports a study of the composition of commercial samples of this material from two industrial scale manufacturers in terms of the structures and relative concentrations of their components, the major of which is perfluoroethylcyclohexanesulfonate (PFECHS). Fractionation of one of these mixtures by column chromatography produced fractions in which all significant components were of sufficient purity to allow assignment of their structures by ¹⁹F NMR spectroscopy. Assessment of the relevant signals in the ¹⁹F NMR spectra of the commercial mixtures by integration revealed the presence of 14 constituents at levels ≥0.5% in terms of molar contributions. Ten of these involve five pairs of geometric isomers, including cis- and trans-PFECHS which accounted for between 55% and 60% of the components present. Three constituents were determined to be isomers of perfluorooctanesulfonate (PFOS), two branched and the other linear PFOS itself. The availability of samples of the various components also allowed us to identify the compounds responsible for the peaks observed when the commercial samples were analyzed by LC/MS using either C₁₈ or perfluorophenyl stationary phases.

(1)H NMR spectroscopic elucidation in solution of the kinetics and thermodynamics of spin crossover for an exceptionally robust Fe(2+) complex

A series of Fe(2+) spin crossover (SCO) complexes [Fe(5/6)](2+) employing hexadentate ligands (5/6) with cis/trans-1,2-diamino cyclohexanes (4) as central building blocks were synthesised. The ligands were obtained by reductive amination of 4 with 2,2'-bipyridyl-6-carbaldehyde or 1,10-phenanthroline-2-carbaldehyde 3. The chelating effect and the rigid structure of the ligands 5/6 lead to exceptionally robust Fe(2+) and Zn(2+) complexes conserving their structure even in coordinating solvents like dmso at high temperatures. Their solution behavior was investigated using variable temperature (VT) (1)H NMR spectroscopy and VT Vis spectroscopy. SCO behavior was found for all Fe(2+) complexes in this series centred around and far above room temperature. For the first time we have demonstrated that the thermodynamics as well as kinetics for SCO can be deduced by using VT (1)H NMR spectroscopy. An alternative scheme using a linear correction term C(1) to model chemical shifts for Fe(2+) SCO complexes is presented. The rate constant for the SCO of [Fe(rac-trans-5)](2+) obtained by VT (1)H NMR was validated by Laser Flash Photolysis (LFP), with excellent agreement (1/(kHL + kLH) = 33.7/35.8 ns for NMR/LFP). The solvent dependence of the transition temperature T1/2 and the solvatochromism of complex [Fe(rac-trans-5)](2+) were ascribed to hydrogen bond formation of the secondary amine to the solvent. Enantiomerically pure complexes can be prepared starting with R,R- or S,S-1,2-diaminocyclohexane (R,R-trans-4 or S,S-trans-4). The high robustness of the complexes reduces a possible ligand scrambling and allows preparation of quasiracemic crystals of [Zn(R,R-5)][Fe(S,S-5)](ClO4)4·(CH3CN) composed of a 1 : 1 mixture of the Zn and Fe complexes with inverse chirality.

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ∼3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.

Antitumor compounds based on a natural product consensus pharmacophore

We report the design and highly enantioselective synthesis of a potent analogue of the spliceosome inhibitor FR901464, based on a non-natural product scaffold. The design of this compound was facilitated by a pharmacophore hypothesis that assumed key interaction types that are common to FR901464 and an otherwise unrelated natural product (pladienolide). The synthesis allows for the preparation of numerous novel analogues. We present results on the in vitro activity for this compound against several tumor cell lines.

Conformational and phase transformations of chlorocyclohexane at high pressures by Raman spectroscopy

Pressure induced conformational and phase transformations of chlorocyclohexane (CCH) were investigated in a diamond anvil cell by Raman spectroscopy at room temperature. Pure CCH was compressed up to 20 GPa and then decompressed to ambient pressure. The conformational equilibrium was shifted by pressure from equatorial to axial conformers in the fluid phase below 0.7 GPa, consistent with previous observations. Upon further compression, several solid-to-solid phase transitions were identified by the observation of markedly different Raman patterns as well as different pressure dependences of characteristic Raman modes. The possible structures of these phases were analyzed in correlation with previously observed solid phases at low temperatures. Finally, CCH exhibits pressure hysteresis and partial reversibility upon decompression which result in the formation of the phases with different Raman patterns from those obtained upon compression. The difference can be interpreted as conformational contribution as well as the intrinsic plasticity of CCH crystals.

Conformational analysis of phorboxazole bis-oxazole oxane fragment analogs by NMR spectroscopy and molecular modeling simulations

We present a detailed conformational study of a simplified synthetic analog of the bis-oxazole oxane fragment found in the cytostatic agents phorboxazole A and B based on results from NMR spectroscopy and molecular modeling simulations. Complete 1H and 13C resonance assignments for the bis-oxazole oxane system were carried out through the use of COSY, HSQC, HMBC, TOCSY, and HSQC-TOCSY experiments, and its conformational preferences in solution were investigated by analysis of 3J(HH) coupling constants and NOE enhancements obtained from 1D and 2D NOESY experiments. In order to solve inconsistencies from our preliminary structural studies, simulated annealing studies were performed to thoroughly sample the phase space available to the molecule. Our results reveal that the six-membered oxane ring, which constitutes the most important moiety regarding the three-dimensional (3D) structure and flexibility of the analog, exists in rapid equilibrium between its two accessible chair conformers in an approximate ratio of 70:30. The information gathered from these studies will be of critical importance in our efforts to prepare novel compounds with phorboxazole-like structure and activity.